Unbiased Discovery & Biofluids
We utilize Data-Independent Acquisition (DIA) on state-of-the-art timsTOF and Orbitrap instruments. Unlike antibody-based panels that only find what you are looking for, our approach digitizes the entire proteome map of your sample.
Biofluid Analysis: Mass Spec vs. O-Link
- Species Agnostic: O-Link is primarily designed for human panels. Our Mass Spec workflows work on any species—mice, rats, agricultural crops, or non-model organisms.
- True Discovery: Targeted panels see the "tip of the iceberg." We detect thousands of proteins without bias, allowing you to discover novel biomarkers you didn't know existed.
- Cost-Effective: Achieve broad coverage for a fraction of the cost of large custom arrays.
Beyond the Transcriptome: Why RNA Is Not Enough
Many researchers rely on RNAseq as a proxy for protein expression. However, current research (e.g., Buccitelli & Selbach, 2020) highlights a significant "Genotype-Phenotype Gap."
The Scientific Reality
- Low Correlation: mRNA levels typically explain only ~40% of the variability in protein levels. The rest is determined by translation efficiency and protein degradation.
- Temporal Disconnect: Proteins are generally more stable than mRNAs. A change in mRNA is often a transient signal, while the protein response persists long after the mRNA is gone.
- Functionality: Proteomics probes the stage of gene expression closer to "gene function" and phenotype.
"Protein levels are more robust against functionally irrelevant mRNA-level variability." — Buccitelli & Selbach, Nat Rev Genet (2020)
Correlation data adapted from Vogel & Marcotte (2012) and Buccitelli & Selbach (2020).
The "Protein Buffering" Effect
Cells actively "buffer" protein levels against genetic noise. In cases of aneuploidy or Copy Number Variations (CNVs), mRNA levels often spike, yet the cell maintains stable protein levels by rapidly degrading excess subunits.
If you rely solely on RNAseq, you may see a "change" that the cell has already corrected. Proteomics reveals the stable, functional reality.
Superior Stability in Clinical Samples
For clinical and archival research, protein stability is a decisive advantage. Unlike mRNA, which degrades rapidly ex vivo, proteins remain stable for long periods.
- FFPE Compatibility: We can extract deep proteomes from Formalin-Fixed Paraffin-Embedded (FFPE) blocks that are decades old.
- Biobank Ready: Ideal for retrospective studies using banked serum, plasma, or tissue where RNA quality may be compromised.
High-Throughput Profiling
KingFisher & Magnetic Bead Technology
Reproducibility is the cornerstone of large-scale proteomics. We have automated our sample preparation pipelines to handle large cohorts with minimal variability.
- Automated Prep: We utilize the Thermo KingFisher Apex robotic platform for automated protein cleanup and digestion.
- MagBead Technology: Using magnetic bead chemistry (SP3/ProTrap), we ensure consistent protein recovery and removal of contaminants (SDS, detergents).
- Scalability: Ideal for clinical studies or large experimental designs (96-well plate format), ensuring that sample 1 and sample 96 are processed exactly the same way.
From Data to Insight
We don't just send you a spreadsheet of accession numbers. Our service includes comprehensive data analysis to help you make biological sense of your results.
- Visualizations: Volcano plots, Heatmaps, and PCA plots included in standard reports.
- Pathway Analysis: GO Term enrichment and pathway mapping to identify affected biological processes.
- Software Support: We utilize industry-standard tools like Spectronaut, DIA-NN, and FragPipe.
Writing a Grant?
Involving the Core early in your grant writing process significantly strengthens your proposal.
- Letters of Support: We provide formal letters detailing our facility's capabilities and commitment to your project.
- Methods Text: Copy-paste ready technical descriptions of our LC-MS/MS workflows and instruments.
- Consultation: We assist with power analysis and experimental design to ensure your budget and sample numbers are robust.
Ready to start your project?
Contact us during the design phase to discuss which workflow best fits your biological question.
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